I Just picked up my TI tonight and I noticed that the rear seat scuppers are not actually solid and don't necessarily line up with the tubes going down to below. It seems that this could lead to a problem with water not leaving the well, but rather entering the hull itself.

Should be fine. Those are protective sleeves that help prevent scupper cart damage. The old boats didn't have them. You're actually less at risk of a problem with your newer boat.

I'm assuming that there is not a hole above the black part, but just a gap, if that's the case I wouldn't worry about things not lining up perfectly. That's pretty close, and from what I understand, the rotomolding process isn't an exact science. If it made it to the dealer, and to you, it's probably passed inspection, and is fine.